Multiple sequence alignment - TraesCS2D01G120400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G120400 chr2D 100.000 5323 0 0 1 5323 69539477 69534155 0.000000e+00 9830.0
1 TraesCS2D01G120400 chr2D 96.341 82 3 0 3531 3612 69535871 69535790 9.300000e-28 135.0
2 TraesCS2D01G120400 chr2D 96.341 82 3 0 3607 3688 69535947 69535866 9.300000e-28 135.0
3 TraesCS2D01G120400 chr2A 91.963 3633 166 40 62 3609 69356362 69352771 0.000000e+00 4975.0
4 TraesCS2D01G120400 chr2A 93.533 866 34 11 3804 4669 69352597 69351754 0.000000e+00 1269.0
5 TraesCS2D01G120400 chr2A 90.300 433 24 9 4903 5323 69351404 69350978 7.790000e-153 551.0
6 TraesCS2D01G120400 chr2A 95.882 170 7 0 4709 4878 69351657 69351488 5.250000e-70 276.0
7 TraesCS2D01G120400 chr2A 91.139 158 10 2 3607 3760 69352849 69352692 1.500000e-50 211.0
8 TraesCS2D01G120400 chr1B 90.444 3380 194 61 283 3609 611931184 611927881 0.000000e+00 4333.0
9 TraesCS2D01G120400 chr1B 92.790 846 41 5 3804 4648 611927708 611926882 0.000000e+00 1206.0
10 TraesCS2D01G120400 chr1B 90.504 337 17 8 4903 5226 611926577 611926243 1.060000e-116 431.0
11 TraesCS2D01G120400 chr1B 91.139 158 10 2 3607 3760 611927959 611927802 1.500000e-50 211.0
12 TraesCS2D01G120400 chr1B 91.339 127 10 1 168 293 611931331 611931205 7.090000e-39 172.0
13 TraesCS2D01G120400 chr1B 90.090 111 11 0 4760 4870 592029554 592029444 1.550000e-30 145.0
14 TraesCS2D01G120400 chr1B 81.250 176 24 7 5020 5187 656851506 656851332 3.340000e-27 134.0
15 TraesCS2D01G120400 chr1B 84.444 135 17 3 4738 4872 656675896 656676026 4.330000e-26 130.0
16 TraesCS2D01G120400 chr1B 84.444 135 17 3 4738 4872 656851792 656851662 4.330000e-26 130.0
17 TraesCS2D01G120400 chr1B 98.077 52 1 0 4709 4760 611926767 611926716 2.040000e-14 91.6
18 TraesCS2D01G120400 chr2B 94.247 1321 64 5 2298 3609 105993740 105992423 0.000000e+00 2008.0
19 TraesCS2D01G120400 chr2B 93.176 850 38 10 3804 4648 105992252 105991418 0.000000e+00 1230.0
20 TraesCS2D01G120400 chr2B 87.922 563 40 17 1630 2171 105994328 105993773 5.810000e-179 638.0
21 TraesCS2D01G120400 chr2B 94.247 365 17 2 725 1089 105995235 105994875 6.020000e-154 555.0
22 TraesCS2D01G120400 chr2B 91.541 331 18 7 5000 5322 105991116 105990788 1.050000e-121 448.0
23 TraesCS2D01G120400 chr2B 87.821 156 16 3 3607 3760 105992501 105992347 4.240000e-41 180.0
24 TraesCS2D01G120400 chr2B 93.684 95 5 1 4906 4999 105991294 105991200 2.000000e-29 141.0
25 TraesCS2D01G120400 chr2B 94.340 53 3 0 4648 4700 105991393 105991341 1.230000e-11 82.4
26 TraesCS2D01G120400 chr2B 90.909 55 3 1 3758 3812 105992332 105992280 7.390000e-09 73.1
27 TraesCS2D01G120400 chr6B 80.667 300 49 8 28 322 276511017 276511312 1.930000e-54 224.0
28 TraesCS2D01G120400 chr1A 94.000 100 6 0 4773 4872 533903428 533903329 9.230000e-33 152.0
29 TraesCS2D01G120400 chr1A 74.179 457 76 28 4759 5187 566410171 566410613 9.230000e-33 152.0
30 TraesCS2D01G120400 chr1A 90.741 108 9 1 4765 4872 533760297 533760191 5.560000e-30 143.0
31 TraesCS2D01G120400 chr1A 81.034 174 24 5 5022 5187 566416081 566416253 4.330000e-26 130.0
32 TraesCS2D01G120400 chr1A 80.000 185 28 3 5011 5187 566413215 566413398 1.560000e-25 128.0
33 TraesCS2D01G120400 chr1A 97.778 45 1 0 4904 4948 533760092 533760048 1.590000e-10 78.7
34 TraesCS2D01G120400 chr1A 95.556 45 2 0 4904 4948 533779229 533779185 7.390000e-09 73.1
35 TraesCS2D01G120400 chr1D 86.014 143 17 3 4738 4877 436972123 436971981 3.320000e-32 150.0
36 TraesCS2D01G120400 chr1D 91.667 108 8 1 4765 4872 436721832 436721726 1.190000e-31 148.0
37 TraesCS2D01G120400 chr1D 85.185 135 16 3 4738 4872 472411136 472411266 9.300000e-28 135.0
38 TraesCS2D01G120400 chr1D 79.167 168 27 5 5022 5182 376866038 376866204 5.640000e-20 110.0
39 TraesCS2D01G120400 chr1D 95.556 45 2 0 4904 4948 436855920 436855876 7.390000e-09 73.1
40 TraesCS2D01G120400 chr5D 86.207 87 10 2 4781 4867 17506589 17506505 5.680000e-15 93.5
41 TraesCS2D01G120400 chr7B 86.364 88 4 4 5019 5098 593925121 593925208 7.340000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G120400 chr2D 69534155 69539477 5322 True 3366.666667 9830 97.560667 1 5323 3 chr2D.!!$R1 5322
1 TraesCS2D01G120400 chr2A 69350978 69356362 5384 True 1456.400000 4975 92.563400 62 5323 5 chr2A.!!$R1 5261
2 TraesCS2D01G120400 chr1B 611926243 611931331 5088 True 1074.100000 4333 92.382167 168 5226 6 chr1B.!!$R2 5058
3 TraesCS2D01G120400 chr2B 105990788 105995235 4447 True 595.055556 2008 91.987444 725 5322 9 chr2B.!!$R1 4597

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
28 29 0.322456 TGGCCATTTCGAAGGAGGTG 60.322 55.000 0.00 0.0 0.00 4.00 F
29 30 0.322546 GGCCATTTCGAAGGAGGTGT 60.323 55.000 7.59 0.0 0.00 4.16 F
433 471 0.466543 ACCAACTTGCACACTACGGA 59.533 50.000 0.00 0.0 0.00 4.69 F
609 685 1.003839 GGGCCACGTCATTGTGAGA 60.004 57.895 4.39 0.0 42.55 3.27 F
973 1088 1.029947 GTTCGTGCTATGGTTGGGGG 61.030 60.000 0.00 0.0 0.00 5.40 F
1317 1444 1.073284 ACGGTTCCACTGCCTTGTTAT 59.927 47.619 0.00 0.0 0.00 1.89 F
1767 2002 1.499502 GCTCTTTCAGCCGCAACTC 59.500 57.895 0.00 0.0 43.17 3.01 F
3124 3396 1.135460 GCTCTGAAGACAAAGCATGCC 60.135 52.381 15.66 0.0 39.60 4.40 F
3802 4094 0.032678 AGAGTGTCCAAGTGAGCACG 59.967 55.000 0.00 0.0 36.99 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1294 1421 0.606401 CAAGGCAGTGGAACCGTGAT 60.606 55.000 0.00 0.0 37.60 3.06 R
1531 1757 2.276732 ACATCACAAAGGACCCACAG 57.723 50.000 0.00 0.0 0.00 3.66 R
1575 1804 2.995466 ACAACAAGCACCATTGATCG 57.005 45.000 0.00 0.0 34.20 3.69 R
2560 2825 0.038892 CAGGTTTCAGGCACATGCAC 60.039 55.000 6.15 0.0 44.36 4.57 R
2624 2890 0.676151 CCTTCAGCTCTGCTTCCACC 60.676 60.000 0.00 0.0 36.40 4.61 R
3055 3326 0.698818 AGTTTAAGTCCCTGGGGCTG 59.301 55.000 22.92 0.0 34.68 4.85 R
3404 3676 0.322008 CAGCAGACCTCCCAAGTTCC 60.322 60.000 0.00 0.0 0.00 3.62 R
4268 4596 0.249868 CCTTCTTGGCAGACACGTCA 60.250 55.000 0.00 0.0 0.00 4.35 R
5160 5728 1.134551 GGTCTGAGAATCCTCACTGGC 60.135 57.143 0.00 0.0 44.01 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.468985 TGGTGGTAATGGCCATTTCG 58.531 50.000 34.85 0.00 41.08 3.46
20 21 1.004862 TGGTGGTAATGGCCATTTCGA 59.995 47.619 34.85 24.11 41.08 3.71
21 22 2.096248 GGTGGTAATGGCCATTTCGAA 58.904 47.619 34.85 18.60 41.08 3.71
22 23 2.099098 GGTGGTAATGGCCATTTCGAAG 59.901 50.000 34.85 0.00 41.08 3.79
23 24 2.099098 GTGGTAATGGCCATTTCGAAGG 59.901 50.000 34.85 0.00 41.08 3.46
24 25 2.025793 TGGTAATGGCCATTTCGAAGGA 60.026 45.455 34.85 13.48 32.81 3.36
25 26 2.618709 GGTAATGGCCATTTCGAAGGAG 59.381 50.000 34.85 0.00 32.50 3.69
26 27 1.767759 AATGGCCATTTCGAAGGAGG 58.232 50.000 25.73 7.76 0.00 4.30
27 28 0.625849 ATGGCCATTTCGAAGGAGGT 59.374 50.000 14.09 0.00 0.00 3.85
28 29 0.322456 TGGCCATTTCGAAGGAGGTG 60.322 55.000 0.00 0.00 0.00 4.00
29 30 0.322546 GGCCATTTCGAAGGAGGTGT 60.323 55.000 7.59 0.00 0.00 4.16
30 31 0.804989 GCCATTTCGAAGGAGGTGTG 59.195 55.000 7.59 0.00 0.00 3.82
31 32 0.804989 CCATTTCGAAGGAGGTGTGC 59.195 55.000 0.00 0.00 0.00 4.57
32 33 1.611673 CCATTTCGAAGGAGGTGTGCT 60.612 52.381 0.00 0.00 0.00 4.40
33 34 2.154462 CATTTCGAAGGAGGTGTGCTT 58.846 47.619 0.00 0.00 36.98 3.91
34 35 2.341846 TTTCGAAGGAGGTGTGCTTT 57.658 45.000 0.00 0.00 33.83 3.51
35 36 2.341846 TTCGAAGGAGGTGTGCTTTT 57.658 45.000 0.00 0.00 33.83 2.27
36 37 1.593196 TCGAAGGAGGTGTGCTTTTG 58.407 50.000 0.00 0.00 33.83 2.44
37 38 1.134220 TCGAAGGAGGTGTGCTTTTGT 60.134 47.619 0.00 0.00 33.83 2.83
38 39 1.676006 CGAAGGAGGTGTGCTTTTGTT 59.324 47.619 0.00 0.00 33.83 2.83
39 40 2.541588 CGAAGGAGGTGTGCTTTTGTTG 60.542 50.000 0.00 0.00 33.83 3.33
40 41 2.143876 AGGAGGTGTGCTTTTGTTGT 57.856 45.000 0.00 0.00 0.00 3.32
41 42 2.024414 AGGAGGTGTGCTTTTGTTGTC 58.976 47.619 0.00 0.00 0.00 3.18
42 43 1.748493 GGAGGTGTGCTTTTGTTGTCA 59.252 47.619 0.00 0.00 0.00 3.58
43 44 2.362077 GGAGGTGTGCTTTTGTTGTCAT 59.638 45.455 0.00 0.00 0.00 3.06
44 45 3.374745 GAGGTGTGCTTTTGTTGTCATG 58.625 45.455 0.00 0.00 0.00 3.07
45 46 2.101249 AGGTGTGCTTTTGTTGTCATGG 59.899 45.455 0.00 0.00 0.00 3.66
46 47 2.159114 GGTGTGCTTTTGTTGTCATGGT 60.159 45.455 0.00 0.00 0.00 3.55
47 48 3.520569 GTGTGCTTTTGTTGTCATGGTT 58.479 40.909 0.00 0.00 0.00 3.67
48 49 3.306703 GTGTGCTTTTGTTGTCATGGTTG 59.693 43.478 0.00 0.00 0.00 3.77
49 50 3.056250 TGTGCTTTTGTTGTCATGGTTGT 60.056 39.130 0.00 0.00 0.00 3.32
50 51 3.932089 GTGCTTTTGTTGTCATGGTTGTT 59.068 39.130 0.00 0.00 0.00 2.83
51 52 5.105752 GTGCTTTTGTTGTCATGGTTGTTA 58.894 37.500 0.00 0.00 0.00 2.41
52 53 5.005299 GTGCTTTTGTTGTCATGGTTGTTAC 59.995 40.000 0.00 0.00 0.00 2.50
53 54 5.105554 TGCTTTTGTTGTCATGGTTGTTACT 60.106 36.000 0.00 0.00 0.00 2.24
54 55 5.458779 GCTTTTGTTGTCATGGTTGTTACTC 59.541 40.000 0.00 0.00 0.00 2.59
55 56 6.680378 GCTTTTGTTGTCATGGTTGTTACTCT 60.680 38.462 0.00 0.00 0.00 3.24
56 57 6.371809 TTTGTTGTCATGGTTGTTACTCTC 57.628 37.500 0.00 0.00 0.00 3.20
57 58 4.385825 TGTTGTCATGGTTGTTACTCTCC 58.614 43.478 0.00 0.00 0.00 3.71
58 59 3.313012 TGTCATGGTTGTTACTCTCCG 57.687 47.619 0.00 0.00 0.00 4.63
59 60 2.894765 TGTCATGGTTGTTACTCTCCGA 59.105 45.455 0.00 0.00 0.00 4.55
60 61 3.513912 TGTCATGGTTGTTACTCTCCGAT 59.486 43.478 0.00 0.00 0.00 4.18
61 62 3.865745 GTCATGGTTGTTACTCTCCGATG 59.134 47.826 0.00 0.00 0.00 3.84
62 63 3.767131 TCATGGTTGTTACTCTCCGATGA 59.233 43.478 0.00 0.00 0.00 2.92
63 64 4.405680 TCATGGTTGTTACTCTCCGATGAT 59.594 41.667 0.00 0.00 0.00 2.45
64 65 4.123497 TGGTTGTTACTCTCCGATGATG 57.877 45.455 0.00 0.00 0.00 3.07
65 66 2.866762 GGTTGTTACTCTCCGATGATGC 59.133 50.000 0.00 0.00 0.00 3.91
66 67 3.430929 GGTTGTTACTCTCCGATGATGCT 60.431 47.826 0.00 0.00 0.00 3.79
67 68 4.202121 GGTTGTTACTCTCCGATGATGCTA 60.202 45.833 0.00 0.00 0.00 3.49
68 69 4.837896 TGTTACTCTCCGATGATGCTAG 57.162 45.455 0.00 0.00 0.00 3.42
80 81 2.356818 GATGCTAGCTCCTTCGGCGT 62.357 60.000 17.23 0.00 34.52 5.68
239 240 2.875933 GTTTGGGTCGTGTCATCTTTGA 59.124 45.455 0.00 0.00 0.00 2.69
290 322 8.292448 TGCACTCTTCTTTCTATCAAATGAAAC 58.708 33.333 0.00 0.00 0.00 2.78
314 346 1.817099 CGGCTCTCCTGCATGGTTC 60.817 63.158 0.00 0.00 37.07 3.62
431 469 2.353269 TGAAACCAACTTGCACACTACG 59.647 45.455 0.00 0.00 0.00 3.51
432 470 1.305201 AACCAACTTGCACACTACGG 58.695 50.000 0.00 0.00 0.00 4.02
433 471 0.466543 ACCAACTTGCACACTACGGA 59.533 50.000 0.00 0.00 0.00 4.69
434 472 1.148310 CCAACTTGCACACTACGGAG 58.852 55.000 0.00 0.00 0.00 4.63
455 493 6.020599 CGGAGTACATTACAAAGACTGATTCG 60.021 42.308 0.00 0.00 0.00 3.34
457 495 4.946784 ACATTACAAAGACTGATTCGCC 57.053 40.909 0.00 0.00 0.00 5.54
458 496 3.689649 ACATTACAAAGACTGATTCGCCC 59.310 43.478 0.00 0.00 0.00 6.13
459 497 3.695830 TTACAAAGACTGATTCGCCCT 57.304 42.857 0.00 0.00 0.00 5.19
485 524 6.765915 AAAAAGGCTGATTGGTCTAAGATC 57.234 37.500 0.00 0.00 0.00 2.75
487 526 3.663198 AGGCTGATTGGTCTAAGATCCT 58.337 45.455 0.00 0.00 0.00 3.24
490 560 5.071115 AGGCTGATTGGTCTAAGATCCTTAC 59.929 44.000 0.00 0.00 0.00 2.34
501 571 6.016108 GTCTAAGATCCTTACCTATGCTCGTT 60.016 42.308 0.00 0.00 0.00 3.85
510 580 3.786635 ACCTATGCTCGTTCATTCACTC 58.213 45.455 0.00 0.00 0.00 3.51
601 677 2.927856 AGGTGATGGGCCACGTCA 60.928 61.111 9.28 7.15 42.69 4.35
609 685 1.003839 GGGCCACGTCATTGTGAGA 60.004 57.895 4.39 0.00 42.55 3.27
612 688 1.071605 GCCACGTCATTGTGAGACTC 58.928 55.000 0.00 0.00 42.55 3.36
617 693 5.171476 CCACGTCATTGTGAGACTCTTATT 58.829 41.667 3.68 0.00 42.55 1.40
642 718 4.641645 CAGCAAGGACGGCCCACA 62.642 66.667 1.76 0.00 37.41 4.17
648 724 4.767255 GGACGGCCCACAGCAGAG 62.767 72.222 0.00 0.00 46.50 3.35
751 850 2.432174 AAACCCTGGCTGCCTTCCTC 62.432 60.000 21.03 0.00 0.00 3.71
759 858 1.271127 GCTGCCTTCCTCCTTCTCCT 61.271 60.000 0.00 0.00 0.00 3.69
796 902 1.725182 TCTTTTCCTCTCCTCCCCTCT 59.275 52.381 0.00 0.00 0.00 3.69
973 1088 1.029947 GTTCGTGCTATGGTTGGGGG 61.030 60.000 0.00 0.00 0.00 5.40
1141 1260 2.006772 CTCGCGTATGGTCAAAGGC 58.993 57.895 5.77 0.00 0.00 4.35
1167 1286 5.917541 TGTTTTGTTTAGTCGACTCATCC 57.082 39.130 23.89 9.29 0.00 3.51
1279 1406 3.738982 TGAGTTACTCATGGGTGTTGTG 58.261 45.455 11.42 0.00 35.39 3.33
1294 1421 3.625764 GTGTTGTGGTTTGCTCTGACTTA 59.374 43.478 0.00 0.00 0.00 2.24
1317 1444 1.073284 ACGGTTCCACTGCCTTGTTAT 59.927 47.619 0.00 0.00 0.00 1.89
1319 1446 2.095263 CGGTTCCACTGCCTTGTTATTG 60.095 50.000 0.00 0.00 0.00 1.90
1321 1448 3.191371 GGTTCCACTGCCTTGTTATTGAG 59.809 47.826 0.00 0.00 0.00 3.02
1324 1451 5.435686 TCCACTGCCTTGTTATTGAGTAT 57.564 39.130 0.00 0.00 0.00 2.12
1326 1453 5.647658 TCCACTGCCTTGTTATTGAGTATTG 59.352 40.000 0.00 0.00 0.00 1.90
1350 1477 3.384467 ACTGTGGTTGTTTTGGAATCAGG 59.616 43.478 0.00 0.00 0.00 3.86
1356 1485 4.176271 GTTGTTTTGGAATCAGGCATAGC 58.824 43.478 0.00 0.00 0.00 2.97
1399 1528 9.325198 ACATGTGTATGTAGTATTATTGTGGTG 57.675 33.333 0.00 0.00 45.45 4.17
1491 1672 9.778741 TCCAAGCCAGTTATTACATAAGATTAG 57.221 33.333 0.00 0.00 0.00 1.73
1531 1757 7.662258 TGTACTAGATATGTGAGAGGCTTAGTC 59.338 40.741 0.00 0.00 0.00 2.59
1575 1804 5.793026 TTTTTGCATGTTTCCTGTTGAAC 57.207 34.783 0.00 0.00 31.05 3.18
1578 1807 2.884012 TGCATGTTTCCTGTTGAACGAT 59.116 40.909 0.00 0.00 31.05 3.73
1622 1852 8.846943 TGTTAAGATTCTTCAGCATTGTCTTA 57.153 30.769 1.27 0.00 0.00 2.10
1628 1858 4.708177 TCTTCAGCATTGTCTTATAGGGC 58.292 43.478 0.00 0.00 0.00 5.19
1664 1894 2.871096 TGTTAAGGGTGCTTACCTGG 57.129 50.000 0.00 0.00 38.63 4.45
1767 2002 1.499502 GCTCTTTCAGCCGCAACTC 59.500 57.895 0.00 0.00 43.17 3.01
1900 2135 1.512926 CTGGTTGGTTTGGAGACTCG 58.487 55.000 0.00 0.00 0.00 4.18
2195 2447 2.532531 ATTTTCATGCTTCGTGCTCG 57.467 45.000 0.81 0.81 43.37 5.03
2258 2511 3.507622 GGTTATGCTCTTCTTTTGGCTGT 59.492 43.478 0.00 0.00 0.00 4.40
2322 2587 7.436080 CACTAATTCATGATTGTGCCCATTTAC 59.564 37.037 0.00 0.00 0.00 2.01
2332 2597 2.417586 GTGCCCATTTACGTAGGTTGAC 59.582 50.000 0.00 0.00 0.00 3.18
2365 2630 4.994744 GCCATTGGCTTGTTGGAC 57.005 55.556 20.66 0.00 46.69 4.02
2581 2846 1.588082 CATGTGCCTGAAACCTGGC 59.412 57.895 6.41 6.41 45.51 4.85
2624 2890 6.257630 GCTTCTTTTAGATACTGCCAGAAGAG 59.742 42.308 0.00 0.00 38.61 2.85
2822 3088 3.056891 CACTTGTTGGTGAACTTGTTGGT 60.057 43.478 0.00 0.00 39.34 3.67
2930 3196 8.911918 AGGTTTGTTGAATTACATACAGTGTA 57.088 30.769 5.24 5.24 42.29 2.90
3022 3289 4.515191 TCATGCTTCTGTGGTTGAAGTTAC 59.485 41.667 0.00 0.00 41.94 2.50
3046 3317 4.807304 CACTTTCTTTTGCTGCAACTGAAT 59.193 37.500 15.72 5.83 0.00 2.57
3055 3326 2.670509 GCTGCAACTGAATTTGAGCTCC 60.671 50.000 12.15 0.00 31.95 4.70
3124 3396 1.135460 GCTCTGAAGACAAAGCATGCC 60.135 52.381 15.66 0.00 39.60 4.40
3202 3474 2.275318 CACAAGGGAAAGATCTCTCGC 58.725 52.381 4.98 4.98 34.38 5.03
3297 3569 3.350219 TGAAAGCAGGATCAAGGTACC 57.650 47.619 2.73 2.73 0.00 3.34
3404 3676 3.254892 GCTTCGAGTTCTTGAGGGTAAG 58.745 50.000 2.25 0.00 0.00 2.34
3517 3789 6.063640 TCCCGCTAAAGTAAGTTGTTTTTC 57.936 37.500 0.00 0.00 0.00 2.29
3543 3815 6.621596 GCTTGCTCTATGTTTCAAAGTGTAGG 60.622 42.308 0.00 0.00 0.00 3.18
3557 3829 3.483421 AGTGTAGGCCAGTTGTTAAACC 58.517 45.455 5.01 0.00 36.94 3.27
3578 3850 5.418676 ACCTTGTCATTTGTCAAAAACAGG 58.581 37.500 18.47 18.47 39.58 4.00
3599 3871 7.108847 ACAGGAGAATTCTCATTTAACTGGAG 58.891 38.462 31.29 15.00 44.60 3.86
3606 3878 9.129532 GAATTCTCATTTAACTGGAGGATGATT 57.870 33.333 0.00 0.00 27.46 2.57
3607 3879 9.484806 AATTCTCATTTAACTGGAGGATGATTT 57.515 29.630 0.00 0.00 27.46 2.17
3608 3880 8.884124 TTCTCATTTAACTGGAGGATGATTTT 57.116 30.769 0.00 0.00 0.00 1.82
3609 3881 8.511604 TCTCATTTAACTGGAGGATGATTTTC 57.488 34.615 0.00 0.00 0.00 2.29
3610 3882 8.108999 TCTCATTTAACTGGAGGATGATTTTCA 58.891 33.333 0.00 0.00 0.00 2.69
3611 3883 8.648698 TCATTTAACTGGAGGATGATTTTCAA 57.351 30.769 0.00 0.00 0.00 2.69
3612 3884 9.087871 TCATTTAACTGGAGGATGATTTTCAAA 57.912 29.630 0.00 0.00 0.00 2.69
3613 3885 9.362539 CATTTAACTGGAGGATGATTTTCAAAG 57.637 33.333 0.00 0.00 0.00 2.77
3614 3886 8.477419 TTTAACTGGAGGATGATTTTCAAAGT 57.523 30.769 0.00 0.00 0.00 2.66
3615 3887 5.972107 ACTGGAGGATGATTTTCAAAGTG 57.028 39.130 0.00 0.00 0.00 3.16
3616 3888 5.388654 ACTGGAGGATGATTTTCAAAGTGT 58.611 37.500 0.00 0.00 0.00 3.55
3617 3889 6.542821 ACTGGAGGATGATTTTCAAAGTGTA 58.457 36.000 0.00 0.00 0.00 2.90
3618 3890 6.656693 ACTGGAGGATGATTTTCAAAGTGTAG 59.343 38.462 0.00 0.00 0.00 2.74
3619 3891 5.945784 TGGAGGATGATTTTCAAAGTGTAGG 59.054 40.000 0.00 0.00 0.00 3.18
3620 3892 5.163612 GGAGGATGATTTTCAAAGTGTAGGC 60.164 44.000 0.00 0.00 0.00 3.93
3621 3893 4.706962 AGGATGATTTTCAAAGTGTAGGCC 59.293 41.667 0.00 0.00 0.00 5.19
3622 3894 4.462483 GGATGATTTTCAAAGTGTAGGCCA 59.538 41.667 5.01 0.00 0.00 5.36
3623 3895 5.393461 GGATGATTTTCAAAGTGTAGGCCAG 60.393 44.000 5.01 0.00 0.00 4.85
3624 3896 4.469657 TGATTTTCAAAGTGTAGGCCAGT 58.530 39.130 5.01 0.00 0.00 4.00
3625 3897 4.892934 TGATTTTCAAAGTGTAGGCCAGTT 59.107 37.500 5.01 0.00 38.38 3.16
3626 3898 4.647424 TTTTCAAAGTGTAGGCCAGTTG 57.353 40.909 5.01 0.00 36.81 3.16
3627 3899 3.290948 TTCAAAGTGTAGGCCAGTTGT 57.709 42.857 5.01 0.00 36.81 3.32
3628 3900 3.290948 TCAAAGTGTAGGCCAGTTGTT 57.709 42.857 5.01 0.00 36.81 2.83
3629 3901 4.425180 TCAAAGTGTAGGCCAGTTGTTA 57.575 40.909 5.01 0.00 36.81 2.41
3630 3902 4.783055 TCAAAGTGTAGGCCAGTTGTTAA 58.217 39.130 5.01 0.00 36.81 2.01
3631 3903 5.194432 TCAAAGTGTAGGCCAGTTGTTAAA 58.806 37.500 5.01 0.00 36.81 1.52
3632 3904 5.066764 TCAAAGTGTAGGCCAGTTGTTAAAC 59.933 40.000 5.01 0.00 36.81 2.01
3633 3905 3.483421 AGTGTAGGCCAGTTGTTAAACC 58.517 45.455 5.01 0.00 36.94 3.27
3634 3906 3.137728 AGTGTAGGCCAGTTGTTAAACCT 59.862 43.478 5.01 0.00 36.94 3.50
3635 3907 3.887110 GTGTAGGCCAGTTGTTAAACCTT 59.113 43.478 5.01 0.00 36.94 3.50
3636 3908 3.886505 TGTAGGCCAGTTGTTAAACCTTG 59.113 43.478 5.01 0.00 36.94 3.61
3637 3909 3.026707 AGGCCAGTTGTTAAACCTTGT 57.973 42.857 5.01 0.00 36.94 3.16
3638 3910 2.956333 AGGCCAGTTGTTAAACCTTGTC 59.044 45.455 5.01 0.00 36.94 3.18
3639 3911 2.691011 GGCCAGTTGTTAAACCTTGTCA 59.309 45.455 0.00 0.00 36.94 3.58
3640 3912 3.320826 GGCCAGTTGTTAAACCTTGTCAT 59.679 43.478 0.00 0.00 36.94 3.06
3641 3913 4.202212 GGCCAGTTGTTAAACCTTGTCATT 60.202 41.667 0.00 0.00 36.94 2.57
3642 3914 5.356426 GCCAGTTGTTAAACCTTGTCATTT 58.644 37.500 0.00 0.00 36.94 2.32
3643 3915 5.234116 GCCAGTTGTTAAACCTTGTCATTTG 59.766 40.000 0.00 0.00 36.94 2.32
3644 3916 6.337356 CCAGTTGTTAAACCTTGTCATTTGT 58.663 36.000 0.00 0.00 36.94 2.83
3645 3917 6.475402 CCAGTTGTTAAACCTTGTCATTTGTC 59.525 38.462 0.00 0.00 36.94 3.18
3646 3918 7.032580 CAGTTGTTAAACCTTGTCATTTGTCA 58.967 34.615 0.00 0.00 36.94 3.58
3647 3919 7.543868 CAGTTGTTAAACCTTGTCATTTGTCAA 59.456 33.333 0.00 0.00 36.94 3.18
3648 3920 8.091449 AGTTGTTAAACCTTGTCATTTGTCAAA 58.909 29.630 0.00 0.00 36.94 2.69
3649 3921 8.713271 GTTGTTAAACCTTGTCATTTGTCAAAA 58.287 29.630 1.31 0.00 0.00 2.44
3650 3922 8.833231 TGTTAAACCTTGTCATTTGTCAAAAA 57.167 26.923 1.31 0.00 0.00 1.94
3651 3923 8.713271 TGTTAAACCTTGTCATTTGTCAAAAAC 58.287 29.630 1.31 4.87 0.00 2.43
3652 3924 8.713271 GTTAAACCTTGTCATTTGTCAAAAACA 58.287 29.630 1.31 7.35 35.59 2.83
3653 3925 6.966435 AACCTTGTCATTTGTCAAAAACAG 57.034 33.333 13.47 8.41 39.58 3.16
3654 3926 6.036577 ACCTTGTCATTTGTCAAAAACAGT 57.963 33.333 13.47 8.86 39.58 3.55
3655 3927 7.164230 ACCTTGTCATTTGTCAAAAACAGTA 57.836 32.000 13.47 3.99 39.58 2.74
3656 3928 7.257722 ACCTTGTCATTTGTCAAAAACAGTAG 58.742 34.615 13.47 10.54 39.58 2.57
3657 3929 7.122055 ACCTTGTCATTTGTCAAAAACAGTAGA 59.878 33.333 13.47 3.24 39.58 2.59
3658 3930 7.973388 CCTTGTCATTTGTCAAAAACAGTAGAA 59.027 33.333 13.47 2.98 39.58 2.10
3659 3931 9.520204 CTTGTCATTTGTCAAAAACAGTAGAAT 57.480 29.630 13.47 0.00 39.58 2.40
3660 3932 9.868277 TTGTCATTTGTCAAAAACAGTAGAATT 57.132 25.926 13.47 0.00 39.58 2.17
3661 3933 9.515020 TGTCATTTGTCAAAAACAGTAGAATTC 57.485 29.630 1.31 0.00 39.58 2.17
3662 3934 9.736023 GTCATTTGTCAAAAACAGTAGAATTCT 57.264 29.630 13.56 13.56 39.58 2.40
3676 3948 9.892130 ACAGTAGAATTCTAATTTAACTGGAGG 57.108 33.333 26.22 11.26 41.17 4.30
3730 4005 7.119262 AGGATGTTACGACTTTGTTCTTATTGG 59.881 37.037 0.00 0.00 0.00 3.16
3740 4015 6.149474 ACTTTGTTCTTATTGGTCAAGATCCG 59.851 38.462 0.00 0.00 32.27 4.18
3765 4057 5.164061 GGCAGATCTAACAATTGCAAAAACG 60.164 40.000 1.71 0.00 36.53 3.60
3802 4094 0.032678 AGAGTGTCCAAGTGAGCACG 59.967 55.000 0.00 0.00 36.99 5.34
3917 4244 5.842907 AGTTTGAAATTTGCCTGACCTTAC 58.157 37.500 0.00 0.00 0.00 2.34
4190 4518 3.378399 GAGCAAGGAGGCCGAGGAC 62.378 68.421 0.00 0.00 0.00 3.85
4268 4596 3.728373 GACGCCCCCATGGAGGTT 61.728 66.667 15.22 0.00 38.44 3.50
4521 4852 4.928615 GTGCTCTCATCTATAACATCTGCC 59.071 45.833 0.00 0.00 0.00 4.85
4594 4925 7.939039 TGCCAATTTTATCCCTTATCTAGTCAG 59.061 37.037 0.00 0.00 0.00 3.51
4595 4926 7.094592 GCCAATTTTATCCCTTATCTAGTCAGC 60.095 40.741 0.00 0.00 0.00 4.26
4596 4927 7.939039 CCAATTTTATCCCTTATCTAGTCAGCA 59.061 37.037 0.00 0.00 0.00 4.41
4597 4928 8.997323 CAATTTTATCCCTTATCTAGTCAGCAG 58.003 37.037 0.00 0.00 0.00 4.24
4598 4929 7.914427 TTTTATCCCTTATCTAGTCAGCAGA 57.086 36.000 0.00 0.00 0.00 4.26
4645 4976 7.996644 TGGGAACAACACTCTTAACTAGATTTT 59.003 33.333 0.00 0.00 37.44 1.82
4647 4978 9.665264 GGAACAACACTCTTAACTAGATTTTTG 57.335 33.333 0.00 0.00 32.48 2.44
4688 5055 1.141019 GCATGACATTGCTGGCAGG 59.859 57.895 17.64 1.38 45.74 4.85
4700 5073 1.755179 CTGGCAGGATCGAACCAAAT 58.245 50.000 14.80 0.00 0.00 2.32
4701 5074 2.094675 CTGGCAGGATCGAACCAAATT 58.905 47.619 14.80 0.00 0.00 1.82
4702 5075 3.278574 CTGGCAGGATCGAACCAAATTA 58.721 45.455 14.80 0.00 0.00 1.40
4704 5077 4.082845 TGGCAGGATCGAACCAAATTAAA 58.917 39.130 14.80 0.00 0.00 1.52
4705 5078 4.524714 TGGCAGGATCGAACCAAATTAAAA 59.475 37.500 14.80 0.00 0.00 1.52
4706 5079 4.862574 GGCAGGATCGAACCAAATTAAAAC 59.137 41.667 14.80 0.00 0.00 2.43
4707 5080 5.465935 GCAGGATCGAACCAAATTAAAACA 58.534 37.500 14.80 0.00 0.00 2.83
4835 5234 2.856000 AGGGGTGGCTTGAGCTGT 60.856 61.111 0.00 0.00 41.70 4.40
4837 5236 2.431683 GGGTGGCTTGAGCTGTCA 59.568 61.111 0.00 0.00 41.70 3.58
4846 5245 3.529533 GCTTGAGCTGTCAGTATGATGT 58.470 45.455 0.93 0.00 42.80 3.06
4953 5427 7.114754 TCTGATGATATGCCTTGTTTTCTTCT 58.885 34.615 0.00 0.00 0.00 2.85
4993 5468 7.428282 TGCGATTGTTTTGAAATAGTAGTCA 57.572 32.000 0.00 0.00 0.00 3.41
5065 5623 5.885912 AGCTTTATGTTGGAATTACCGTCAT 59.114 36.000 0.00 0.00 42.61 3.06
5187 5755 4.478203 TGAGGATTCTCAGACCATAGGAG 58.522 47.826 0.00 0.00 44.39 3.69
5189 5757 2.029470 GGATTCTCAGACCATAGGAGCG 60.029 54.545 0.00 0.00 0.00 5.03
5241 5809 4.402474 GCCTTGCTGACCCTATATTTTGTT 59.598 41.667 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.004862 TCGAAATGGCCATTACCACCA 59.995 47.619 30.84 9.56 44.17 4.17
1 2 1.757682 TCGAAATGGCCATTACCACC 58.242 50.000 30.84 15.82 44.17 4.61
2 3 2.099098 CCTTCGAAATGGCCATTACCAC 59.901 50.000 30.84 19.62 44.17 4.16
3 4 2.025793 TCCTTCGAAATGGCCATTACCA 60.026 45.455 30.84 14.51 45.82 3.25
4 5 2.618709 CTCCTTCGAAATGGCCATTACC 59.381 50.000 30.84 22.66 0.00 2.85
6 7 2.241176 ACCTCCTTCGAAATGGCCATTA 59.759 45.455 30.84 13.48 0.00 1.90
7 8 1.005924 ACCTCCTTCGAAATGGCCATT 59.994 47.619 25.73 25.73 0.00 3.16
8 9 0.625849 ACCTCCTTCGAAATGGCCAT 59.374 50.000 14.09 14.09 0.00 4.40
9 10 0.322456 CACCTCCTTCGAAATGGCCA 60.322 55.000 8.56 8.56 0.00 5.36
10 11 0.322546 ACACCTCCTTCGAAATGGCC 60.323 55.000 0.00 0.00 0.00 5.36
11 12 0.804989 CACACCTCCTTCGAAATGGC 59.195 55.000 0.00 0.00 0.00 4.40
12 13 0.804989 GCACACCTCCTTCGAAATGG 59.195 55.000 0.00 4.31 0.00 3.16
13 14 1.813513 AGCACACCTCCTTCGAAATG 58.186 50.000 0.00 0.00 0.00 2.32
14 15 2.568623 AAGCACACCTCCTTCGAAAT 57.431 45.000 0.00 0.00 0.00 2.17
15 16 2.341846 AAAGCACACCTCCTTCGAAA 57.658 45.000 0.00 0.00 0.00 3.46
16 17 1.946768 CAAAAGCACACCTCCTTCGAA 59.053 47.619 0.00 0.00 0.00 3.71
17 18 1.134220 ACAAAAGCACACCTCCTTCGA 60.134 47.619 0.00 0.00 0.00 3.71
18 19 1.308998 ACAAAAGCACACCTCCTTCG 58.691 50.000 0.00 0.00 0.00 3.79
19 20 2.427095 ACAACAAAAGCACACCTCCTTC 59.573 45.455 0.00 0.00 0.00 3.46
20 21 2.427095 GACAACAAAAGCACACCTCCTT 59.573 45.455 0.00 0.00 0.00 3.36
21 22 2.024414 GACAACAAAAGCACACCTCCT 58.976 47.619 0.00 0.00 0.00 3.69
22 23 1.748493 TGACAACAAAAGCACACCTCC 59.252 47.619 0.00 0.00 0.00 4.30
23 24 3.374745 CATGACAACAAAAGCACACCTC 58.625 45.455 0.00 0.00 0.00 3.85
24 25 2.101249 CCATGACAACAAAAGCACACCT 59.899 45.455 0.00 0.00 0.00 4.00
25 26 2.159114 ACCATGACAACAAAAGCACACC 60.159 45.455 0.00 0.00 0.00 4.16
26 27 3.163630 ACCATGACAACAAAAGCACAC 57.836 42.857 0.00 0.00 0.00 3.82
27 28 3.056250 ACAACCATGACAACAAAAGCACA 60.056 39.130 0.00 0.00 0.00 4.57
28 29 3.520569 ACAACCATGACAACAAAAGCAC 58.479 40.909 0.00 0.00 0.00 4.40
29 30 3.883830 ACAACCATGACAACAAAAGCA 57.116 38.095 0.00 0.00 0.00 3.91
30 31 5.348164 AGTAACAACCATGACAACAAAAGC 58.652 37.500 0.00 0.00 0.00 3.51
31 32 6.795399 AGAGTAACAACCATGACAACAAAAG 58.205 36.000 0.00 0.00 0.00 2.27
32 33 6.183360 GGAGAGTAACAACCATGACAACAAAA 60.183 38.462 0.00 0.00 0.00 2.44
33 34 5.298276 GGAGAGTAACAACCATGACAACAAA 59.702 40.000 0.00 0.00 0.00 2.83
34 35 4.819630 GGAGAGTAACAACCATGACAACAA 59.180 41.667 0.00 0.00 0.00 2.83
35 36 4.385825 GGAGAGTAACAACCATGACAACA 58.614 43.478 0.00 0.00 0.00 3.33
36 37 3.432252 CGGAGAGTAACAACCATGACAAC 59.568 47.826 0.00 0.00 0.00 3.32
37 38 3.322541 TCGGAGAGTAACAACCATGACAA 59.677 43.478 0.00 0.00 0.00 3.18
38 39 2.894765 TCGGAGAGTAACAACCATGACA 59.105 45.455 0.00 0.00 0.00 3.58
39 40 3.587797 TCGGAGAGTAACAACCATGAC 57.412 47.619 0.00 0.00 0.00 3.06
40 41 3.767131 TCATCGGAGAGTAACAACCATGA 59.233 43.478 0.00 0.00 43.63 3.07
41 42 4.123497 TCATCGGAGAGTAACAACCATG 57.877 45.455 0.00 0.00 43.63 3.66
42 43 4.697514 CATCATCGGAGAGTAACAACCAT 58.302 43.478 0.00 0.00 43.63 3.55
43 44 3.678806 GCATCATCGGAGAGTAACAACCA 60.679 47.826 0.00 0.00 43.63 3.67
44 45 2.866762 GCATCATCGGAGAGTAACAACC 59.133 50.000 0.00 0.00 43.63 3.77
45 46 3.786635 AGCATCATCGGAGAGTAACAAC 58.213 45.455 0.00 0.00 43.63 3.32
46 47 4.499865 GCTAGCATCATCGGAGAGTAACAA 60.500 45.833 10.63 0.00 43.63 2.83
47 48 3.004839 GCTAGCATCATCGGAGAGTAACA 59.995 47.826 10.63 0.00 43.63 2.41
48 49 3.254657 AGCTAGCATCATCGGAGAGTAAC 59.745 47.826 18.83 0.00 43.63 2.50
49 50 3.491342 AGCTAGCATCATCGGAGAGTAA 58.509 45.455 18.83 0.00 43.63 2.24
50 51 3.078097 GAGCTAGCATCATCGGAGAGTA 58.922 50.000 18.83 0.00 43.63 2.59
51 52 1.885887 GAGCTAGCATCATCGGAGAGT 59.114 52.381 18.83 0.00 43.63 3.24
52 53 1.202114 GGAGCTAGCATCATCGGAGAG 59.798 57.143 18.83 0.00 43.63 3.20
53 54 1.202989 AGGAGCTAGCATCATCGGAGA 60.203 52.381 18.83 0.00 45.75 3.71
54 55 1.255882 AGGAGCTAGCATCATCGGAG 58.744 55.000 18.83 0.00 0.00 4.63
55 56 1.615883 GAAGGAGCTAGCATCATCGGA 59.384 52.381 18.83 0.00 0.00 4.55
56 57 1.668337 CGAAGGAGCTAGCATCATCGG 60.668 57.143 18.83 4.28 0.00 4.18
57 58 1.695813 CGAAGGAGCTAGCATCATCG 58.304 55.000 18.83 17.21 0.00 3.84
80 81 2.799017 AGCATGAAAGCAATGACCAGA 58.201 42.857 0.00 0.00 36.85 3.86
239 240 0.105408 AAGAAGGCACCGTACAACGT 59.895 50.000 0.00 0.00 40.58 3.99
290 322 3.200593 GCAGGAGAGCCGCATGTG 61.201 66.667 0.00 0.00 39.96 3.21
336 371 3.074412 CAAAGTGCCTTTGTATCGGACT 58.926 45.455 15.52 0.00 43.85 3.85
431 469 6.237861 GCGAATCAGTCTTTGTAATGTACTCC 60.238 42.308 0.00 0.00 0.00 3.85
432 470 6.237861 GGCGAATCAGTCTTTGTAATGTACTC 60.238 42.308 0.00 0.00 0.00 2.59
433 471 5.581085 GGCGAATCAGTCTTTGTAATGTACT 59.419 40.000 0.00 0.00 0.00 2.73
434 472 5.220605 GGGCGAATCAGTCTTTGTAATGTAC 60.221 44.000 0.00 0.00 0.00 2.90
481 520 4.215908 TGAACGAGCATAGGTAAGGATCT 58.784 43.478 0.00 0.00 0.00 2.75
484 523 4.404394 TGAATGAACGAGCATAGGTAAGGA 59.596 41.667 0.00 0.00 0.00 3.36
485 524 4.508124 GTGAATGAACGAGCATAGGTAAGG 59.492 45.833 0.00 0.00 0.00 2.69
487 526 5.339008 AGTGAATGAACGAGCATAGGTAA 57.661 39.130 0.00 0.00 0.00 2.85
490 560 2.791560 CGAGTGAATGAACGAGCATAGG 59.208 50.000 0.00 0.00 0.00 2.57
521 591 4.590487 CACGTGAACGGGCATAGT 57.410 55.556 10.90 0.00 44.95 2.12
528 598 3.458579 CGTCGAGCACGTGAACGG 61.459 66.667 22.23 8.04 44.07 4.44
576 652 1.566298 GGCCCATCACCTCAAGACCT 61.566 60.000 0.00 0.00 0.00 3.85
582 658 2.927856 ACGTGGCCCATCACCTCA 60.928 61.111 0.00 0.00 34.36 3.86
601 677 4.384647 GGCCTGGAATAAGAGTCTCACAAT 60.385 45.833 1.94 0.00 0.00 2.71
609 685 0.548510 GCTGGGCCTGGAATAAGAGT 59.451 55.000 12.70 0.00 0.00 3.24
612 688 1.396653 CTTGCTGGGCCTGGAATAAG 58.603 55.000 17.19 2.93 0.00 1.73
617 693 3.650950 GTCCTTGCTGGGCCTGGA 61.651 66.667 12.70 6.53 33.37 3.86
742 841 0.117140 TGAGGAGAAGGAGGAAGGCA 59.883 55.000 0.00 0.00 0.00 4.75
751 850 4.148825 CGCGGGGTGAGGAGAAGG 62.149 72.222 0.00 0.00 0.00 3.46
778 877 1.273896 GGAGAGGGGAGGAGAGGAAAA 60.274 57.143 0.00 0.00 0.00 2.29
832 938 2.577700 CTGTGTATAGGAGGACGAGCT 58.422 52.381 0.00 0.00 0.00 4.09
963 1078 2.213513 CGGCAAAACCCCCAACCAT 61.214 57.895 0.00 0.00 33.26 3.55
973 1088 4.999939 CGCACCTGCCGGCAAAAC 63.000 66.667 32.09 18.53 37.91 2.43
1124 1243 1.807981 CGCCTTTGACCATACGCGA 60.808 57.895 15.93 0.00 42.03 5.87
1141 1260 5.552807 TGAGTCGACTAAACAAAACAAACG 58.447 37.500 20.09 0.00 0.00 3.60
1167 1286 0.934436 CGAACCAAAAGCACGGCAAG 60.934 55.000 0.00 0.00 0.00 4.01
1279 1406 2.673368 CCGTGATAAGTCAGAGCAAACC 59.327 50.000 0.00 0.00 34.36 3.27
1294 1421 0.606401 CAAGGCAGTGGAACCGTGAT 60.606 55.000 0.00 0.00 37.60 3.06
1317 1444 7.415765 CCAAAACAACCACAGTACAATACTCAA 60.416 37.037 0.00 0.00 36.76 3.02
1319 1446 6.261381 TCCAAAACAACCACAGTACAATACTC 59.739 38.462 0.00 0.00 36.76 2.59
1321 1448 6.380095 TCCAAAACAACCACAGTACAATAC 57.620 37.500 0.00 0.00 0.00 1.89
1324 1451 5.419155 TGATTCCAAAACAACCACAGTACAA 59.581 36.000 0.00 0.00 0.00 2.41
1326 1453 5.507315 CCTGATTCCAAAACAACCACAGTAC 60.507 44.000 0.00 0.00 0.00 2.73
1356 1485 6.384224 ACACATGTTTCTGCATTAACAGATG 58.616 36.000 15.99 16.61 45.75 2.90
1399 1528 6.393171 AGATTGAAACTTTATCAAAGCAGCC 58.607 36.000 0.00 0.00 42.27 4.85
1500 1681 6.442952 CCTCTCACATATCTAGTACAACAGC 58.557 44.000 0.00 0.00 0.00 4.40
1531 1757 2.276732 ACATCACAAAGGACCCACAG 57.723 50.000 0.00 0.00 0.00 3.66
1575 1804 2.995466 ACAACAAGCACCATTGATCG 57.005 45.000 0.00 0.00 34.20 3.69
1578 1807 4.199432 ACAAAACAACAAGCACCATTGA 57.801 36.364 0.00 0.00 34.20 2.57
1622 1852 3.330701 TGAACCAACAAAGAGAGCCCTAT 59.669 43.478 0.00 0.00 0.00 2.57
1628 1858 6.294176 CCCTTAACATGAACCAACAAAGAGAG 60.294 42.308 0.00 0.00 0.00 3.20
1664 1894 8.700644 CATTACGGCAAGTCAGTAATACTAATC 58.299 37.037 0.00 0.00 41.80 1.75
2282 2536 8.935844 TCATGAATTAGTGTAGCTTTACTTGTG 58.064 33.333 7.72 1.14 0.00 3.33
2283 2537 9.672673 ATCATGAATTAGTGTAGCTTTACTTGT 57.327 29.630 0.00 0.00 0.00 3.16
2322 2587 6.273071 TGAATGATCATAGTGTCAACCTACG 58.727 40.000 9.04 0.00 0.00 3.51
2332 2597 4.217767 CCAATGGCCTGAATGATCATAGTG 59.782 45.833 9.04 0.76 34.37 2.74
2365 2630 4.092091 GTGTTAAGCTCCTTGTCAAGATCG 59.908 45.833 14.42 3.17 0.00 3.69
2560 2825 0.038892 CAGGTTTCAGGCACATGCAC 60.039 55.000 6.15 0.00 44.36 4.57
2581 2846 6.192234 AGAAGCAGAAGCAATCACTTAATG 57.808 37.500 0.00 0.00 45.49 1.90
2624 2890 0.676151 CCTTCAGCTCTGCTTCCACC 60.676 60.000 0.00 0.00 36.40 4.61
2822 3088 1.679139 CATGGGAAATAAGGCGAGCA 58.321 50.000 0.00 0.00 0.00 4.26
3022 3289 2.861935 CAGTTGCAGCAAAAGAAAGTGG 59.138 45.455 10.11 0.00 0.00 4.00
3025 3292 5.978934 AATTCAGTTGCAGCAAAAGAAAG 57.021 34.783 21.04 5.77 0.00 2.62
3029 3300 4.318546 GCTCAAATTCAGTTGCAGCAAAAG 60.319 41.667 10.11 5.54 34.53 2.27
3046 3317 2.759114 CTGGGGCTGGAGCTCAAA 59.241 61.111 17.19 1.72 45.20 2.69
3055 3326 0.698818 AGTTTAAGTCCCTGGGGCTG 59.301 55.000 22.92 0.00 34.68 4.85
3297 3569 1.403780 GCCTCTACACCACGGTAACAG 60.404 57.143 0.00 0.00 0.00 3.16
3404 3676 0.322008 CAGCAGACCTCCCAAGTTCC 60.322 60.000 0.00 0.00 0.00 3.62
3517 3789 4.153986 CACTTTGAAACATAGAGCAAGCG 58.846 43.478 0.00 0.00 0.00 4.68
3543 3815 4.584327 ATGACAAGGTTTAACAACTGGC 57.416 40.909 0.00 0.00 32.90 4.85
3557 3829 6.563422 TCTCCTGTTTTTGACAAATGACAAG 58.437 36.000 14.71 10.85 37.93 3.16
3578 3850 7.989741 TCATCCTCCAGTTAAATGAGAATTCTC 59.010 37.037 25.68 25.68 43.15 2.87
3599 3871 4.462483 TGGCCTACACTTTGAAAATCATCC 59.538 41.667 3.32 0.00 0.00 3.51
3606 3878 3.626930 ACAACTGGCCTACACTTTGAAA 58.373 40.909 3.32 0.00 0.00 2.69
3607 3879 3.290948 ACAACTGGCCTACACTTTGAA 57.709 42.857 3.32 0.00 0.00 2.69
3608 3880 3.290948 AACAACTGGCCTACACTTTGA 57.709 42.857 3.32 0.00 0.00 2.69
3609 3881 5.278604 GTTTAACAACTGGCCTACACTTTG 58.721 41.667 3.32 0.72 0.00 2.77
3610 3882 4.340097 GGTTTAACAACTGGCCTACACTTT 59.660 41.667 3.32 0.00 32.90 2.66
3611 3883 3.887110 GGTTTAACAACTGGCCTACACTT 59.113 43.478 3.32 0.00 32.90 3.16
3612 3884 3.137728 AGGTTTAACAACTGGCCTACACT 59.862 43.478 3.32 0.00 32.90 3.55
3613 3885 3.483421 AGGTTTAACAACTGGCCTACAC 58.517 45.455 3.32 0.00 32.90 2.90
3614 3886 3.868619 AGGTTTAACAACTGGCCTACA 57.131 42.857 3.32 0.00 32.90 2.74
3615 3887 3.887110 ACAAGGTTTAACAACTGGCCTAC 59.113 43.478 3.32 0.00 32.90 3.18
3616 3888 4.139038 GACAAGGTTTAACAACTGGCCTA 58.861 43.478 3.32 0.00 32.90 3.93
3617 3889 2.956333 GACAAGGTTTAACAACTGGCCT 59.044 45.455 3.32 0.00 32.90 5.19
3618 3890 2.691011 TGACAAGGTTTAACAACTGGCC 59.309 45.455 0.00 0.00 32.90 5.36
3619 3891 4.584327 ATGACAAGGTTTAACAACTGGC 57.416 40.909 0.00 0.00 32.90 4.85
3620 3892 6.337356 ACAAATGACAAGGTTTAACAACTGG 58.663 36.000 0.00 0.00 32.90 4.00
3621 3893 7.032580 TGACAAATGACAAGGTTTAACAACTG 58.967 34.615 0.00 0.00 32.90 3.16
3622 3894 7.164230 TGACAAATGACAAGGTTTAACAACT 57.836 32.000 0.00 0.00 32.90 3.16
3623 3895 7.820044 TTGACAAATGACAAGGTTTAACAAC 57.180 32.000 0.00 0.00 0.00 3.32
3624 3896 8.833231 TTTTGACAAATGACAAGGTTTAACAA 57.167 26.923 0.50 0.00 32.04 2.83
3625 3897 8.713271 GTTTTTGACAAATGACAAGGTTTAACA 58.287 29.630 0.50 0.00 32.04 2.41
3626 3898 8.713271 TGTTTTTGACAAATGACAAGGTTTAAC 58.287 29.630 12.59 6.15 34.69 2.01
3627 3899 8.833231 TGTTTTTGACAAATGACAAGGTTTAA 57.167 26.923 12.59 0.00 34.69 1.52
3628 3900 8.091449 ACTGTTTTTGACAAATGACAAGGTTTA 58.909 29.630 14.71 0.00 37.93 2.01
3629 3901 6.934083 ACTGTTTTTGACAAATGACAAGGTTT 59.066 30.769 14.71 1.17 37.93 3.27
3630 3902 6.463360 ACTGTTTTTGACAAATGACAAGGTT 58.537 32.000 14.71 2.83 37.93 3.50
3631 3903 6.036577 ACTGTTTTTGACAAATGACAAGGT 57.963 33.333 14.71 9.71 37.93 3.50
3632 3904 7.479980 TCTACTGTTTTTGACAAATGACAAGG 58.520 34.615 14.71 9.28 37.93 3.61
3633 3905 8.909708 TTCTACTGTTTTTGACAAATGACAAG 57.090 30.769 14.71 11.56 37.93 3.16
3634 3906 9.868277 AATTCTACTGTTTTTGACAAATGACAA 57.132 25.926 14.71 0.00 37.93 3.18
3635 3907 9.515020 GAATTCTACTGTTTTTGACAAATGACA 57.485 29.630 13.69 13.69 37.93 3.58
3636 3908 9.736023 AGAATTCTACTGTTTTTGACAAATGAC 57.264 29.630 6.06 4.93 37.93 3.06
3650 3922 9.892130 CCTCCAGTTAAATTAGAATTCTACTGT 57.108 33.333 22.97 14.04 37.66 3.55
3668 3940 9.933723 CTTTCAATTAAAAATCATCCTCCAGTT 57.066 29.630 0.00 0.00 0.00 3.16
3669 3941 9.312904 TCTTTCAATTAAAAATCATCCTCCAGT 57.687 29.630 0.00 0.00 0.00 4.00
3730 4005 3.297391 GATCTGCCCGGATCTTGAC 57.703 57.895 0.73 0.00 39.06 3.18
3740 4015 4.454728 TTTGCAATTGTTAGATCTGCCC 57.545 40.909 5.18 0.00 31.92 5.36
3765 4057 7.803659 GGACACTCTTAATTAACAGCAAGTTTC 59.196 37.037 0.82 1.15 41.64 2.78
3802 4094 2.287373 GCTCTGTGACAGAATATGCAGC 59.713 50.000 16.94 10.54 40.18 5.25
3833 4160 2.416747 GGAAATCCAAAAGCTGTTGGC 58.583 47.619 28.39 15.35 46.56 4.52
3890 4217 6.012745 AGGTCAGGCAAATTTCAAACTCTAT 58.987 36.000 0.00 0.00 0.00 1.98
3917 4244 7.471721 TGTAAGTCTGACAATGACAAACAAAG 58.528 34.615 10.88 0.00 36.94 2.77
4059 4387 4.504916 CTCCTGCTCGCCGTCCTG 62.505 72.222 0.00 0.00 0.00 3.86
4190 4518 3.297620 GTGTTGGCTGCAGGGGTG 61.298 66.667 17.12 0.00 0.00 4.61
4266 4594 1.261619 CTTCTTGGCAGACACGTCAAC 59.738 52.381 0.00 0.00 0.00 3.18
4268 4596 0.249868 CCTTCTTGGCAGACACGTCA 60.250 55.000 0.00 0.00 0.00 4.35
4329 4660 2.285083 CAAATTTCCGGCGTATCTCCA 58.715 47.619 6.01 0.00 0.00 3.86
4339 4670 3.056891 AGCATTACACCACAAATTTCCGG 60.057 43.478 0.00 0.00 0.00 5.14
4521 4852 6.556212 ACTACTCGACAGAATGAACATACTG 58.444 40.000 0.00 0.00 39.69 2.74
4594 4925 1.999735 TGCGCAGTAAGTGTAATCTGC 59.000 47.619 5.66 6.02 46.38 4.26
4595 4926 2.604914 CCTGCGCAGTAAGTGTAATCTG 59.395 50.000 33.75 11.55 0.00 2.90
4596 4927 2.418746 CCCTGCGCAGTAAGTGTAATCT 60.419 50.000 33.75 0.00 0.00 2.40
4597 4928 1.933853 CCCTGCGCAGTAAGTGTAATC 59.066 52.381 33.75 0.00 0.00 1.75
4598 4929 1.553248 TCCCTGCGCAGTAAGTGTAAT 59.447 47.619 33.75 0.00 0.00 1.89
4611 4942 1.303236 TGTTGTTCCCATCCCTGCG 60.303 57.895 0.00 0.00 0.00 5.18
4645 4976 5.718146 TGCAACAACAAGAATCAAAGTCAA 58.282 33.333 0.00 0.00 0.00 3.18
4647 4978 5.332808 GCATGCAACAACAAGAATCAAAGTC 60.333 40.000 14.21 0.00 0.00 3.01
4654 5018 3.991773 GTCATGCATGCAACAACAAGAAT 59.008 39.130 26.68 0.00 0.00 2.40
4688 5055 8.026607 TGGAGAATGTTTTAATTTGGTTCGATC 58.973 33.333 0.00 0.00 0.00 3.69
4700 5073 8.296713 CCGAGAAAGATTTGGAGAATGTTTTAA 58.703 33.333 0.00 0.00 0.00 1.52
4701 5074 7.574967 GCCGAGAAAGATTTGGAGAATGTTTTA 60.575 37.037 0.00 0.00 0.00 1.52
4702 5075 6.681777 CCGAGAAAGATTTGGAGAATGTTTT 58.318 36.000 0.00 0.00 0.00 2.43
4704 5077 4.156739 GCCGAGAAAGATTTGGAGAATGTT 59.843 41.667 0.00 0.00 0.00 2.71
4705 5078 3.691609 GCCGAGAAAGATTTGGAGAATGT 59.308 43.478 0.00 0.00 0.00 2.71
4706 5079 3.944015 AGCCGAGAAAGATTTGGAGAATG 59.056 43.478 0.00 0.00 0.00 2.67
4707 5080 3.944015 CAGCCGAGAAAGATTTGGAGAAT 59.056 43.478 0.00 0.00 0.00 2.40
4835 5234 6.093082 CAGTTGCAAAGATGACATCATACTGA 59.907 38.462 17.57 0.00 36.57 3.41
4837 5236 6.175471 TCAGTTGCAAAGATGACATCATACT 58.825 36.000 17.57 3.44 36.57 2.12
4846 5245 5.988310 AATGGATTCAGTTGCAAAGATGA 57.012 34.783 0.00 3.22 0.00 2.92
4938 5412 5.596836 AAATGTCAGAAGAAAACAAGGCA 57.403 34.783 0.00 0.00 0.00 4.75
5010 5568 3.550820 TGGCTTCAATTGCGGTACATAT 58.449 40.909 0.00 0.00 0.00 1.78
5011 5569 2.992593 TGGCTTCAATTGCGGTACATA 58.007 42.857 0.00 0.00 0.00 2.29
5012 5570 1.832883 TGGCTTCAATTGCGGTACAT 58.167 45.000 0.00 0.00 0.00 2.29
5065 5623 5.468746 AGAAAGCCGCAAAAATATCGCTATA 59.531 36.000 0.00 0.00 0.00 1.31
5160 5728 1.134551 GGTCTGAGAATCCTCACTGGC 60.135 57.143 0.00 0.00 44.01 4.85
5187 5755 3.898517 AAGAAACAAAACTAGAGCCGC 57.101 42.857 0.00 0.00 0.00 6.53
5189 5757 7.009265 GTGAAACAAAGAAACAAAACTAGAGCC 59.991 37.037 0.00 0.00 36.32 4.70
5261 5829 7.048512 GTCAACCTCTGGCTAATTAGTAATGT 58.951 38.462 13.91 2.34 0.00 2.71
5264 5832 5.724854 AGGTCAACCTCTGGCTAATTAGTAA 59.275 40.000 13.91 2.21 44.77 2.24
5265 5833 5.278061 AGGTCAACCTCTGGCTAATTAGTA 58.722 41.667 13.91 3.32 44.77 1.82
5272 5843 2.570302 GGTTTAGGTCAACCTCTGGCTA 59.430 50.000 4.63 0.00 44.77 3.93


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.